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RESCUE-ESE specifications

Information


Unique identifier OMICS_09615
Name RESCUE-ESE
Interface Web user interface
Restrictions to use None
Input data RNA, DNA sequences
Input format FASTA, Raw
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chris Burge

Publications for RESCUE-ESE

RESCUE-ESE citations

 (134)
library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] script with the Alamut Visual Software (Interactive Software, Rouen, France), which contains the algorithms SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder, ESE-Finder, and RESCUE-ESE. Mutation data from all TCGA series were retrieved from the GDC portal in day 29th of September 2017. Frequencies of germline mutations in general population were retrieved from the ExAC da […]

library_books

Genetic variants of ALDH2 rs671 and CYP2E1 rs2031920 contributed to risk of hepatocellular carcinoma susceptibility in a Chinese population

2018
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105

[…] cts, ESS recruits many proteins that negatively affect the splicing mechanism.Prediction results of changing splicing regulation were also determined with four tools: ESEfinder, ESRSearchi, PESX, and RESCUE_ESE. Abnormal splicing changes are thought to contribute to cancer onset and progression.– These splicing changes induce a nonsynonymous mutation at the rs671 site. The protein coding tools Pol […]

library_books

A Comprehensive in Silico Analysis of Regulatory SNPs of Human CLEC7A Gene and Its Validation as Genotypic and Phenotypic Disease Marker in Recurrent Vulvovaginal Infections

2018
PMCID: 5869923
PMID: 29616193
DOI: 10.3389/fcimb.2018.00065

[…] /). SNPinfo comprises of different sets of data processing elements for the selection of functional SNPs. FuncPred, the main tool of SNPinfo is composite of different singleton tools including SNP3D, rescue ESE, MATCH, miRanda, Polyphen, TRANSFAC12.1, miRBase, FAS–ESS, and ESEfinder (Xu and Taylor, ). RegulomeDB divides functional SNPs into six different classes ranging from C1 to C6. Class 1 SNPs […]

library_books

Coordinated expression and genetic polymorphisms in Grainyhead like genes in human non melanoma skin cancers

2018
BMC Cancer
PMCID: 5755140
PMID: 29301499
DOI: 10.1186/s12885-017-3943-8

[…] esence of these SNPs may be damaging for the functioning of the GRHL3 gene by affecting the processing of primary transcript. We employed two algorithms to search for exonic splicing enhancers (ESE). RESCUE-ESE [] did not detect any potential ESEs that would overlap with the location of SNP rs141193530 or rs151326764. ESEfinder3.0 [] predicted some changes in binding of serine and arginine rich sp […]

library_books

Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent 2 Disease

2018
Genes
PMCID: 5793168
PMID: 29300302
DOI: 10.3390/genes9010015

[…] aluating precisely how mutations influence the loss or gain of splicing regulatory elements (ESEs or ESSs) and its effects on pre-mRNA splicing is more complicated, and the algorithms available, like RESCUE-ESE, ESEfinder and MutPred Splice [,,], still present considerable degrees of inaccuracy [,,]. Therefore, their findings need to be confirmed using experimental methods. The ideal experimental […]

library_books

Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β type hemoglobinopathy patients

2017
Hum Genomics
PMCID: 5654038
PMID: 29061162
DOI: 10.1186/s40246-017-0120-8

[…] silico analyses, rs3024997 (G>A) was found to occur in a deep intronic position, resulting on the activation of an intronic cryptic acceptor site and thus, potential alteration of splicing. Yet, the RESCUE ESE, EIEs, PESE Octamers, ESE Finder-SRp40, and ESR Sequences prediction algorithms suggested the creation of an exonic splicing enhancer, which has probably no impact on splicing. rs2146323 (C […]

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RESCUE-ESE institution(s)
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA

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